Evaluation of Alignment Methods for Genomic Analysis in HPC Environment


KIPS Transactions on Software and Data Engineering, Vol. 2, No. 2, pp. 107-112, Feb. 2013
10.3745/KTSDE.2013.2.2.107,   PDF Download:

Abstract

With the progress of NGS technologies, large genome data have been exploded recently. To analyze such data effectively, the assistance of HPC technique is necessary. In this paper, we organized a genome analysis pipeline to call SNP from NGS data. To organize the pipeline efficiently under HPC environment, we analyzed the CPU utilization pattern of each pipeline steps. We found that sequence alignment is computing centric and suitable for parallelization. We also analyzed the performance of parallel open source alignment tools and found that alignment method utilizing many-core processor can improve the performance of genome analysis pipeline.


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Cite this article
[IEEE Style]
M. G. Lim, H. Y. Jung, M. H. Kim, J. H. Choi, S. J. Park, W. Choi, K. C. Lee, "Evaluation of Alignment Methods for Genomic Analysis in HPC Environment," KIPS Transactions on Software and Data Engineering, vol. 2, no. 2, pp. 107-112, 2013. DOI: 10.3745/KTSDE.2013.2.2.107.

[ACM Style]
Myun Geun Lim, Ho Youl Jung, Min Ho Kim, Jae Hun Choi, Soo Jun Park, Wan Choi, and Kyu Chul Lee. 2013. Evaluation of Alignment Methods for Genomic Analysis in HPC Environment. KIPS Transactions on Software and Data Engineering, 2, 2, (2013), 107-112. DOI: 10.3745/KTSDE.2013.2.2.107.